Question: (Closed) Charateristics Of Strand-Specific Rna-Seq Dataset
0
gravatar for Shaojiang Cai
24 months ago by
Singapore
Shaojiang Cai60 wrote:

Dear all,

I would like to ask the difference between strand-specific and not strand-specific dataset.

As far as I know, strand-specific data means that we know which strand the transcript is from.

I do not have biological background. Please confirm whether it is correct. If we have a transcript, which is from sense strand, when RNA-seq is producing reads, is that first the cDNA is synthesised. Then this cDNA is used for PCR to amplify the sample? Then the reads generated could be from both strands of the original DNA?

For strand-specific protocols, what is different?

ADD COMMENTlink written 24 months ago by Shaojiang Cai60

You need to clarify what are your after, the experimental protocols that are used to prepare samples in a certain way (biostar is not the right forum for that) or the analysis of data that needs to be interpreted in a strand specific manner

ADD REPLYlink written 24 months ago by Istvan Albert ♦♦ 39k

"strand-specific protocols" suggests a molecular biology question, so I'm closing this as off-topic.

ADD REPLYlink written 24 months ago by Neilfws41k
1

How can it be off-topic when the protocol directly determines that nature of the data that will be produced, and must be known by the person preforming the bioinformatic analysis? Anyone doing bioinformatic analysis of an RNA Seq data set must be aware of how to tell what protocol was used, and when a strand specific protocol is necessary to answer certain questions. This person is clearly asking how RNA Seq data differs when strand-specific and non-strand specific protocols are used to generate the data.

ADD REPLYlink written 24 months ago by seidel4.5k

Fine, re-opened. My impression was that it's a molecular biology question but maybe I'm wrong.

ADD REPLYlink written 24 months ago by Neilfws41k

closed again, as the cross-post on the Biology SE has received an accepted answer

ADD REPLYlink written 24 months ago by Michael Kuhn4.7k
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